Journal: Briefings in Bioinformatics

Volume 23, Issue 6

0 -- 0Anna Eames Seffernick, Krzysztof Mrózek, Deedra Nicolet, Richard M. Stone, Ann-Katherin Eisfeld, John C. Byrd, Kellie J. Archer. High-dimensional genomic feature selection with the ordered stereotype logit model
0 -- 0Yanting Zhang, Hisanori Kiryu. MODEC: an unsupervised clustering method integrating omics data for identifying cancer subtypes
0 -- 0Atlas M. Sardoo, Shaoqiang Zhang, Thomas N. Ferraro, Thomas M. Keck, Yong Chen. Decoding brain memory formation by single-cell RNA sequencing
0 -- 0Siyu Han, Xiao Yang, Hang Sun, Hu Yang, Qi Zhang, Cheng Peng, Wensi Fang, Ying Li. LION: an integrated R package for effective prediction of ncRNA-protein interaction
0 -- 0César R. García-Jacas, Luis A. García-González, Felix Martinez-Rios, Issac P. Tapia-Contreras, Carlos A. Brizuela. Handcrafted versus non-handcrafted (self-supervised) features for the classification of antimicrobial peptides: complementary or redundant?
0 -- 0Ricky Wai Tak Leung, Xiaosen Jiang, Xueqing Zong, Yanhong Zhang, Xinlin Hu, Yaohua Hu, Jing Qin 0004. CORN - Condition Orientated Regulatory Networks: bridging conditions to gene networks
0 -- 0Hui Chong, Yuguo Zha, Qingyang Yu, Mingyue Cheng, Guangzhou Xiong, Nan Wang, Xinhe Huang, Shijuan Huang, Chuqing Sun, Sicheng Wu, Wei-Hua Chen, Luís Pedro Coelho, Kang Ning 0001. EXPERT: transfer learning-enabled context-aware microbial community classification
0 -- 0Yansen Su, Minglu Wang, Pengpeng Wang, Chunhou Zheng, Yuansheng Liu, Xiangxiang Zeng. Deep learning joint models for extracting entities and relations in biomedical: a survey and comparison
0 -- 0Vandana Ravindran, Jessica Wagoner, Paschalis Athanasiadis, Andreas B. Den Hartigh, Julia M. Sidorova, Aleksandr Ianevski, Susan L. Fink, Arnoldo Frigessi, Judith White, Stephen J. Polyak, Tero Aittokallio. Discovery of host-directed modulators of virus infection by probing the SARS-CoV-2-host protein-protein interaction network
0 -- 0Qingxia Yang, Bo Li 0097, Panpan Wang, Jicheng Xie, Yuhao Feng, Ziqiang Liu, Feng Zhu 0004. LargeMetabo: an out-of-the-box tool for processing and analyzing large-scale metabolomic data
0 -- 0Yiming Fang, Xuejun Liu, Hui Liu. Attention-aware contrastive learning for predicting T cell receptor-antigen binding specificity
0 -- 0Ziyan Feng, Zihao Shen, Honglin Li, Shiliang Li. e-TSN: an interactive visual exploration platform for target-disease knowledge mapping from literature
0 -- 0Zhen Tian, Xiangyu Peng, Haichuan Fang, Wenjie Zhang, Qiguo Dai, Yangdong Ye. MHADTI: predicting drug-target interactions via multiview heterogeneous information network embedding with hierarchical attention mechanisms
0 -- 0Junyan Song, Pei Fen Kuan. A systematic assessment of cell type deconvolution algorithms for DNA methylation data
0 -- 0Xudong Zhao 0002, Jingwen Zhai, Tong Liu 0013, Guohua Wang. Ensemble classification based feature selection: a case of identification on plant pentatricopeptide repeat proteins
0 -- 0Visanu Wanchai, Piroon Jenjaroenpun, Thongpan Leangapichart, Gerard Arrey, Charles M. Burnham, Maria C. Tümmler, Jesus Delgado-Calle, Birgitte Regenberg, Intawat Nookaew. CReSIL: accurate identification of extrachromosomal circular DNA from long-read sequences
0 -- 0Su Wang, Miran Kim, Wentao Li, Xiaoqian Jiang, Han Chen, Arif Ozgun Harmanci. Privacy-aware estimation of relatedness in admixed populations
0 -- 0Yixuan Qiao, Lianhe Zhao, Chunlong Luo, Yufan Luo, Yang Wu, Shengtong Li, Dechao Bu, Yi Zhao. Multi-modality artificial intelligence in digital pathology
0 -- 0Shidi Miao, Haobo Jia, Ke Cheng, Xiaohui Hu, Jing Li, Wenjuan Huang, Ruitao Wang. Deep learning radiomics under multimodality explore association between muscle/fat and metastasis and survival in breast cancer patients
0 -- 0Benjamin Goudey, Nicholas Geard, Karin Verspoor, Justin Zobel. Propagation, detection and correction of errors using the sequence database network
0 -- 0Binsheng He, Kun Wang, Ju Xiang, Pingping Bing, Min Tang, Geng Tian, Cheng Guo, Miao Xu, Jialiang Yang. DGHNE: network enhancement-based method in identifying disease-causing genes through a heterogeneous biomedical network
0 -- 0Xiu-Ju George Zhao, Hui Cao. Linking research of biomedical datasets
0 -- 0Tang Li, Yanbin Yin. Critical assessment of pan-genomic analysis of metagenome-assembled genomes
0 -- 0Hanyu Zhang, Yunxia Wang, Ziqi Pan, Xiuna Sun, Minjie Mou, Bing Zhang, Zhaorong Li, Honglin Li, Feng Zhu 0004. ncRNAInter: a novel strategy based on graph neural network to discover interactions between lncRNA and miRNA
0 -- 0Yu Xu, Jiaxing Chen, Aiping Lyu, William K. Cheung, Lu Zhang. dynDeepDRIM: a dynamic deep learning model to infer direct regulatory interactions using time-course single-cell gene expression data
0 -- 0Xiaohui Shi, Huajing Teng, Zhongsheng Sun. An updated overview of experimental and computational approaches to identify non-canonical DNA/RNA structures with emphasis on G-quadruplexes and R-loops
0 -- 0Duy Pham, Buu Truong, Khai Tran, Guiyan Ni, Dat Nguyen, Trang T. H. Tran, Mai H. Tran, Duong Thuy Nguyen 0001, Nam S. Vo, Quan Nguyen. Assessing polygenic risk score models for applications in populations with under-represented genomics data: an example of Vietnam
0 -- 0Simon Zhongyuan Tian, Guoliang Li, Duo Ning, Kai Jing, Yewen Xu, Yang Yang, Melissa J. Fullwood, Pengfei Yin, Guangyu Huang, Dariusz Plewczynski, Jixian Zhai, Ziwei Dai, Wei Chen, Meizhen Zheng. MCIBox: a toolkit for single-molecule multi-way chromatin interaction visualization and micro-domains identification
0 -- 0Laura Marchetti, Riccardo Nifosì, Pier Luigi Martelli, Eleonora Da Pozzo, Valentina Cappello, Francesco Banterle, Maria Letizia Trincavelli, Claudia Martini, Massimo D'Elia. Quantum computing algorithms: getting closer to critical problems in computational biology
0 -- 0Dailin Gan, Guosheng Yin, Yan Dora Zhang. The GR2D2 estimator for the precision matrices
0 -- 0Jiaxin Fan, Yafei Lyu, Qihuang Zhang, Xuran Wang, Mingyao Li, Rui Xiao. MuSiC2: cell-type deconvolution for multi-condition bulk RNA-seq data
0 -- 0Caimao Zhou, Dejun Peng, Bo Liao, Ranran Jia, Fang-Xiang Wu. ACP_MS: prediction of anticancer peptides based on feature extraction
0 -- 0Qianmu Yuan, Sheng Chen, Yu Wang, Huiying Zhao, Yuedong Yang. Alignment-free metal ion-binding site prediction from protein sequence through pretrained language model and multi-task learning
0 -- 0Caiwei Zhen, Yuxian Wang, Jiaquan Geng, Lu Han, Jingyi Li, Jinghao Peng, Tao Wang, Jianye Hao, Xuequn Shang, Zhongyu Wei, Peican Zhu, Jiajie Peng. A review and performance evaluation of clustering frameworks for single-cell Hi-C data
0 -- 0Peng Zhang, Shikui Tu, Wen Zhang, Lei Xu. Predicting cell line-specific synergistic drug combinations through a relational graph convolutional network with attention mechanism
0 -- 0Hao Zhang, Nan Zhang, Wantao Wu, Ran Zhou, Shuyu Li, Zeyu Wang, Ziyu Dai, Liyang Zhang, Zaoqu Liu, Jian Zhang, Peng Luo, Zhixiong Liu, Quan Cheng. Machine learning-based tumor-infiltrating immune cell-associated lncRNAs for predicting prognosis and immunotherapy response in patients with glioblastoma
0 -- 0Zeynab Maghsoudi, Ha Nguyen, Alireza Tavakkoli, Tin Nguyen. A comprehensive survey of the approaches for pathway analysis using multi-omics data integration
0 -- 0Jiacheng Leng, Ling-Yun Wu. Interaction-based transcriptome analysis via differential network inference
0 -- 0Kai-Yao Huang, Hui-Ju Kao, Tzu-Hsiang Weng, Chia-Hung Chen, Shun-Long Weng. iDVIP: identification and characterization of viral integrase inhibitory peptides
0 -- 0Meng Zhang, Jian Zhao 0034, Chen Li, Fang Ge, Jing Wu, Bin Jiang, Jiangning Song, Xiaofeng Song. csORF-finder: an effective ensemble learning framework for accurate identification of multi-species coding short open reading frames
0 -- 0Li Peng, Yuan Tu, Li Huang, Yang Li, Xiangzheng Fu, Xiang Chen. DAESTB: inferring associations of small molecule-miRNA via a scalable tree boosting model based on deep autoencoder
0 -- 0Linlin Zhuo, Bosheng Song, Yuansheng Liu, Zejun Li, Xiangzheng Fu. Predicting ncRNA-protein interactions based on dual graph convolutional network and pairwise learning
0 -- 0Julio Vera, Xin Lai 0002, Andreas Baur, Michael Erdmann, Shailendra K. Gupta, Cristiano Guttà, Lucie Heinzerling, Markus V. Heppt, Philipp Maximilian Kazmierczak, Manfred Kunz, Christopher Lischer, Brigitte M. Pützer, Markus Rehm, Christian Ostalecki, Jimmy Retzlaff, Stephan Witt, Olaf Wolkenhauer, Carola Berking. Melanoma 2.0. Skin cancer as a paradigm for emerging diagnostic technologies, computational modelling and artificial intelligence
0 -- 0Lijun Wu, Chengcan Yin, Jinhua Zhu, Zhen Wu, Liang He, Yingce Xia, Shufang Xie 0003, Tao Qin, Tie-Yan Liu. SPRoBERTa: protein embedding learning with local fragment modeling
0 -- 0Menglan Cai, Anna Vesely, Xu Chen, Limin Li, Jelle J. Goeman. NetTDP: permutation-based true discovery proportions for differential co-expression network analysis
0 -- 0Bodhayan Prasad, Anthony J. Bjourson, Priyank Shukla. Data-driven patient stratification of UK Biobank cohort suggests five endotypes of multimorbidity
0 -- 0Jitong Feng, Shengbo Wu, Hongpeng Yang, Chengwei Ai, Jianjun Qiao, Junhai Xu, Fei Guo 0001. Microbe-bridged disease-metabolite associations identification by heterogeneous graph fusion
0 -- 0Yangyang Hao, Liang Lu, Anna Liu, Xue Lin, Li Xiao, Xiaoyue Kong, Kai Li, Fengji Liang, Jianghui Xiong, Lina Qu, Yinghui Li, Jian Li. Integrating bioinformatic strategies in spatial life science research
0 -- 0Anna Christine Haber, Ulrich Sax, Fabian Prasser. Open tools for quantitative anonymization of tabular phenotype data: literature review
0 -- 0Yang Li, Xue-Gang Hu, Lei Wang 0121, Pei-Pei Li, Zhu-Hong You. MNMDCDA: prediction of circRNA-disease associations by learning mixed neighborhood information from multiple distances
0 -- 0Medha Pandey, P. Anoosha, Dhanusha Yesudhas, M. Michael Gromiha. Identification of potential driver mutations in glioblastoma using machine learning
0 -- 0Elias Orouji, Ayush T. Raman. Computational methods to explore chromatin state dynamics
0 -- 0Xing Chen 0001, Li Huang. Computational model for ncRNA research
0 -- 0Hongwei Tu, Yanqiang Han, Zhilong Wang, Jinjin Li. Clustered tree regression to learn protein energy change with mutated amino acid
0 -- 0Yi Zhou, Xinyi Wang, Lin Yao, Min Zhu. LDAformer: predicting lncRNA-disease associations based on topological feature extraction and Transformer encoder
0 -- 0Yaojia Chen, Jiacheng Wang, Chuyu Wang, Mingxin Liu, Quan Zou. Deep learning models for disease-associated circRNA prediction: a review
0 -- 0. Correction to: A comprehensive benchmarking of WGS-based deletion structural variant callers
0 -- 0Trishala Das, Harbinder Kaur, Pratibha Gour, Kartikay Prasad, Andrew M. Lynn, Amresh Prakash, Vijay Kumar. Intersection of network medicine and machine learning towards investigating the key biomarkers and pathways underlying amyotrophic lateral sclerosis: a systematic review
0 -- 0Stephen Bonner, Ian P. Barrett, Cheng Ye, Rowan Swiers, Ola Engkvist, Andreas Bender 0002, Charles Tapley Hoyt, William L. Hamilton. A review of biomedical datasets relating to drug discovery: a knowledge graph perspective
0 -- 0Bo-Wei Zhao, Xiao-Rui Su, Peng-Wei Hu, Yu-Peng Ma, Xi Zhou, Lun Hu. A geometric deep learning framework for drug repositioning over heterogeneous information networks
0 -- 0Julien Tremblay, Lars Schreiber, Charles W. Greer. High-resolution shotgun metagenomics: the more data, the better?
0 -- 0Jie Wang, Zihao Shen, Yichen Liao, Zhen Yuan, Shiliang Li, Gaoqi He, Man Lan, Xuhong Qian, Kai Zhang, Honglin Li. Multi-modal chemical information reconstruction from images and texts for exploring the near-drug space
0 -- 0Qiao Ning, Zedong Qi, Yue Wang, Ansheng Deng, Chen Chen. FCCCSR_Glu: a semi-supervised learning model based on FCCCSR algorithm for prediction of glutarylation sites
0 -- 0Zena Cai, Ping Fu, Ye Qiu, Aiping Wu, Gaihua Zhang, Yirong Wang, Taijiao Jiang, Xing-Yi Ge, Haizhen Zhu, Yousong Peng. vsRNAfinder: a novel method for identifying high-confidence viral small RNAs from small RNA-Seq data
0 -- 0Yuyao Huang, Jiesi Luo, Runyu Jing, Menglong Li. Multi-model predictive analysis of RNA solvent accessibility based on modified residual attention mechanism
0 -- 0Yue Gao 0004, Shipeng Shang, Shuang Guo, Xinyue Wang, Hanxiao Zhou, Yue Sun, Jing Gan, Yakun Zhang, Xia Li, Shangwei Ning, Yunpeng Zhang. AgingBank: a manually curated knowledgebase and high-throughput analysis platform that provides experimentally supported multi-omics data relevant to aging in multiple species
0 -- 0Ebony Rose Watson, Ariane Mora, Atefeh Taherian-Fard, Jessica Cara Mar. How does the structure of data impact cell-cell similarity? Evaluating how structural properties influence the performance of proximity metrics in single cell RNA-seq data
0 -- 0Xia-an Bi, Yuhua Mao, Sheng Luo, Hao Wu, Lixia Zhang, Xun Luo, Luyun Xu. A novel generation adversarial network framework with characteristics aggregation and diffusion for brain disease classification and feature selection
0 -- 0Shamima Rashid, Teng Ann Ng, Chee-Keong Kwoh 0001. Jupytope: computational extraction of structural properties of viral epitopes
0 -- 0Lei Huang, Jiecong Lin, Rui Liu, Zetian Zheng, Lingkuan Meng, Xingjian Chen, Xiangtao Li, Ka Chun Wong. CoaDTI: multi-modal co-attention based framework for drug-target interaction annotation
0 -- 0Jiannan Yang, Zhen Li, William Ka Kei Wu, Shi Yu, Zhongzhi Xu, Qian Chu, Qingpeng Zhang. Deep learning identifies explainable reasoning paths of mechanism of action for drug repurposing from multilayer biological network
0 -- 0Yuhua Yao, Yaping Lv, Ling Tong, Yuebin Liang, Shuxue Xi, Binbin Ji, Guanglu Zhang, Ling Li, Geng Tian, Min Tang, Xiyue Hu, Shijun Li, Jialiang Yang. ICSDA: a multi-modal deep learning model to predict breast cancer recurrence and metastasis risk by integrating pathological, clinical and gene expression data
0 -- 0Meihong Gao, Shuhui Liu, Yang Qi, Xinpeng Guo, Xuequn Shang. GAE-LGA: integration of multi-omics data with graph autoencoders to identify lncRNA-PCG associations
0 -- 0Li Huang, Li Zhang, Xing Chen 0001. Updated review of advances in microRNAs and complex diseases: towards systematic evaluation of computational models
0 -- 0Timothy Warwick, Sandra Seredinski, Nina M. Krause, Jasleen Kaur Bains, Lara Althaus, James A Oo, Alessandro Bonetti, Anne Dueck, Stefan Engelhardt, Harald Schwalbe, Matthias S. Leisegang, Marcel H. Schulz, Ralf P. Brandes. A universal model of RNA.DNA: DNA triplex formation accurately predicts genome-wide RNA-DNA interactions
0 -- 0Tianyang Zhang, Qiang Tang, Fulei Nie, Qi Zhao, Wei Chen. DeepLncPro: an interpretable convolutional neural network model for identifying long non-coding RNA promoters
0 -- 0Bao-Min Liu, Ying-Lian Gao, Dai-Jun Zhang, Feng Zhou, Juan Wang 0003, Chun-Hou Zheng 0001, Jin-Xing Liu. A new framework for drug-disease association prediction combing light-gated message passing neural network and gated fusion mechanism
0 -- 0Jian Ruan, Shuaishuai Xu, Ruyin Chen, Wenxin Qu, Qiong Li, Chanqi Ye, Wei Wu, Qi Jiang, Feifei Yan, Enhui Shen, Qinjie Chu, Yunlu Jia, Xiaochen Zhang, Wenguang Fu, Jinzhang Chen, Michael P. Timko, Peng Zhao, Longjiang Fan, Yifei Shen. EMLI-ICC: an ensemble machine learning-based integration algorithm for metastasis prediction and risk stratification in intrahepatic cholangiocarcinoma
0 -- 0Kai Zheng 0020, Xin-Lu Zhang, Lei Wang 0121, Zhu-Hong You, Zhao-Hui Zhan, Hao-Yuan Li. Line graph attention networks for predicting disease-associated Piwi-interacting RNAs
0 -- 0Li Huang, Li Zhang, Xing Chen 0001. Updated review of advances in microRNAs and complex diseases: experimental results, databases, webservers and data fusion
0 -- 0Chengkui Zhao, Nan Xu, Jingwen Tan, Qi Cheng, Weixin Xie, Jiayu Xu, Zhenyu Wei, Jing Ye, Lei Yu, Weixing Feng. ILGBMSH: an interpretable classification model for the shRNA target prediction with ensemble learning algorithm
0 -- 0. Correction: Insights from analyses of low complexity regions with canonical methods for protein sequence comparison
0 -- 0Liang Cheng. Omics data analysis and integration for COVID-19 patients - editorial
0 -- 0Oskar Hickl, Pedro Queirós, Paul Wilmes, Patrick May, Anna Heintz-Buschart. binny: an automated binning algorithm to recover high-quality genomes from complex metagenomic datasets
0 -- 0Wenkai Yan, Zutan Li, Cong Pian, Yufeng Wu. PlantBind: an attention-based multi-label neural network for predicting plant transcription factor binding sites
0 -- 0Hock Chuan Yeo, Kumar Selvarajoo. Machine learning alternative to systems biology should not solely depend on data
0 -- 0Yue Bi, Fuyi Li, Xudong Guo, Zhikang Wang, Tong Pan, Yuming Guo, Geoffrey I. Webb, Jianhua Yao 0001, Cangzhi Jia, Jiangning Song. Clarion is a multi-label problem transformation method for identifying mRNA subcellular localizations
0 -- 0Renqian Luo, Liai Sun, Yingce Xia, Tao Qin, Sheng Zhang 0012, Hoifung Poon, Tie-Yan Liu. BioGPT: generative pre-trained transformer for biomedical text generation and mining
0 -- 0Jiahui Ji, Maryam Anwar, Enrico Petretto, Costanza Emanueli, Prashant Kumar Srivastava. PPMS: A framework to Profile Primary MicroRNAs from Single-cell RNA-sequencing datasets
0 -- 0Dong Ou-Yang, Yong Liang 0001, Jianjun Wang, Xiao-Ying Liu 0001, Shengli Xie, Rui Miao, Ning Ai, Le Li, Qi Dang. Predicting multiple types of miRNA-disease associations using adaptive weighted nonnegative tensor factorization with self-paced learning and hypergraph regularization
0 -- 0Hang Cheng, Yuhong Sun, Qing Yang, Minggui Deng, Zhijian Yu, Gang Zhu, Jiuxin Qu, Lei Liu, Liang Yang, Yu Xia. A rapid bacterial pathogen and antimicrobial resistance diagnosis workflow using Oxford nanopore adaptive sequencing method
0 -- 0Siqi Chen, Tiancheng Li, Luna Yang, Fei Zhai, Xiwei Jiang, Rongwu Xiang, Guixia Ling. Artificial intelligence-driven prediction of multiple drug interactions
0 -- 0Xizhi Luo, Fei Qin, Feifei Xiao, Guoshuai Cai. BISC: accurate inference of transcriptional bursting kinetics from single-cell transcriptomic data
0 -- 0Yanzheng Meng, Lin Zhang, Laizhi Zhang, Ziyu Wang, Xuanwen Wang, Chan Li, Yu Chen, Shipeng Shang, Lei Li 0013. CysModDB: a comprehensive platform with the integration of manually curated resources and analysis tools for cysteine posttranslational modifications
0 -- 0Wenya Wang, Li Zhang, Jianqiang Sun, Qi Zhao, Jianwei Shuai. Predicting the potential human lncRNA-miRNA interactions based on graph convolution network with conditional random field
0 -- 0Hanxuan Cai, Huimin Zhang, Duancheng Zhao, Jingxing Wu, Ling Wang 0008. FP-GNN: a versatile deep learning architecture for enhanced molecular property prediction
0 -- 0Daniel Rivas-Barragan, Daniel Domingo-Fernández, Yojana Gadiya, David Healey. Ensembles of knowledge graph embedding models improve predictions for drug discovery
0 -- 0Peihao Fan, Julia Kofler, Ying Ding, Michael Marks, Robert A Sweet, Lirong Wang. Efficacy difference of antipsychotics in Alzheimer's disease and schizophrenia: explained with network efficiency and pathway analysis methods
0 -- 0Yuqing Qian, Yijie Ding, Quan Zou 0001, Fei Guo 0001. Identification of drug-side effect association via restricted Boltzmann machines with penalized term
0 -- 0Li Zhang, Chun-Chun Wang, Xing Chen 0001. Predicting drug-target binding affinity through molecule representation block based on multi-head attention and skip connection
0 -- 0Yuan Zhang, Qiaoyan Jiang, Ling Li, Zutan Li, Zhihui Xu, Yuanyuan Chen, Yang Sun, Cheng Liu, Zhengsheng Mao, Feng Chen, Hualan Li, Yue Cao, Cong Pian. Predicting the structure of unexplored novel fentanyl analogues by deep learning model
0 -- 0Chong Jin, Brian Lee, Li Shen, Qi Long. Integrating multi-omics summary data using a Mendelian randomization framework